YDZA - BACSU - GREMLIN Contacts

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YDZA - Uncharacterized membrane protein YdzA

UniProt:	O31485	Sequences: MLHTPIGRLRTMGFIEGMSLLILLFIAMPLKYWAGLPLAVTIVGSVHGGLFILYLLVLAYATFSVKWPLKWSAAGFIAAFVPFGNFLYDRGLRNYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	96 (90)
Sequences:	639 (447)
Seq/√Len:	47.1

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_L	75_G	2.678	1.00
27_A	40_V	2.471	1.00
41_T	45_S	2.467	1.00
28_M	32_Y	2.188	1.00
8_R	60_Y	2.187	1.00
45_S	49_G	2.096	1.00
59_A	63_F	2.092	1.00
62_T	72_S	1.951	0.99
20_L	80_F	1.942	0.99
28_M	43_V	1.918	0.99
30_L	34_A	1.888	0.99
27_A	39_A	1.859	0.99
31_K	40_V	1.736	0.98
25_F	29_P	1.706	0.98
17_G	83_F	1.703	0.98
20_L	85_N	1.685	0.98
26_I	29_P	1.607	0.97
22_I	43_V	1.594	0.97
52_I	56_L	1.581	0.97
23_L	27_A	1.580	0.97
76_F	80_F	1.550	0.97
38_L	42_I	1.499	0.96
75_G	88_Y	1.477	0.96
9_L	13_G	1.469	0.95
16_E	50_L	1.449	0.95
58_L	76_F	1.436	0.95
9_L	54_Y	1.409	0.94
23_L	40_V	1.388	0.94
90_R	94_N	1.366	0.93
13_G	78_A	1.340	0.93
40_V	44_G	1.337	0.92
43_V	46_V	1.335	0.92
36_L	39_A	1.323	0.92
20_L	24_L	1.298	0.91
19_S	50_L	1.298	0.91
13_G	85_N	1.287	0.91
14_F	18_M	1.268	0.90
16_E	19_S	1.256	0.90
9_L	61_A	1.213	0.88
72_S	76_F	1.211	0.88
84_G	89_D	1.175	0.87
30_L	36_L	1.170	0.86
42_I	45_S	1.132	0.84
30_L	39_A	1.096	0.82
17_G	85_N	1.093	0.82
55_L	76_F	1.082	0.82
68_P	71_W	1.062	0.80
60_Y	64_S	1.058	0.80
12_M	53_L	1.052	0.80
20_L	79_A	1.015	0.77
67_W	71_W	1.006	0.77
58_L	72_S	1.002	0.76
56_L	60_Y	0.997	0.76
16_E	84_G	0.994	0.76
29_P	33_W	0.982	0.75
20_L	81_V	0.968	0.74
55_L	59_A	0.953	0.73
42_I	81_V	0.918	0.70
31_K	44_G	0.913	0.69
28_M	46_V	0.911	0.69
74_A	92_L	0.893	0.68
7_G	10_R	0.879	0.66
74_A	91_G	0.873	0.66
84_G	88_Y	0.845	0.63
73_A	77_I	0.839	0.63
18_M	22_I	0.839	0.63
50_L	74_A	0.795	0.59
10_R	46_V	0.795	0.59
66_K	81_V	0.791	0.58
24_L	29_P	0.786	0.58
88_Y	91_G	0.780	0.57
69_L	73_A	0.756	0.55
54_Y	79_A	0.755	0.55
8_R	12_M	0.750	0.54
11_T	78_A	0.748	0.54
16_E	79_A	0.730	0.52
22_I	26_I	0.730	0.52
6_I	52_I	0.730	0.52
39_A	42_I	0.727	0.52
61_A	65_V	0.719	0.51
39_A	43_V	0.718	0.51
51_F	85_N	0.704	0.50
59_A	66_K	0.702	0.49
22_I	25_F	0.696	0.49
5_P	68_P	0.693	0.48
16_E	51_F	0.686	0.48
8_R	56_L	0.684	0.48
41_T	49_G	0.679	0.47
59_A	90_R	0.660	0.45
30_L	37_P	0.658	0.45
81_V	85_N	0.658	0.45
9_L	84_G	0.653	0.45
27_A	37_P	0.646	0.44
46_V	49_G	0.642	0.43
43_V	50_L	0.642	0.43
26_I	31_K	0.637	0.43
88_Y	93_R	0.636	0.43
19_S	44_G	0.632	0.42
53_L	68_P	0.628	0.42
6_I	14_F	0.620	0.41
39_A	45_S	0.615	0.41
9_L	67_W	0.614	0.41
75_G	78_A	0.612	0.41
21_L	49_G	0.611	0.40
18_M	86_F	0.610	0.40
7_G	56_L	0.590	0.38
61_A	75_G	0.586	0.38
51_F	84_G	0.575	0.37
34_A	59_A	0.575	0.37
14_F	92_L	0.571	0.37
71_W	79_A	0.569	0.36
38_L	41_T	0.566	0.36
74_A	88_Y	0.566	0.36
61_A	64_S	0.557	0.35
18_M	60_Y	0.554	0.35
24_L	80_F	0.552	0.35
11_T	15_I	0.551	0.35
8_R	11_T	0.545	0.34
87_L	92_L	0.543	0.34
27_A	41_T	0.542	0.34
8_R	72_S	0.537	0.34
61_A	93_R	0.533	0.33
6_I	92_L	0.530	0.33
16_E	93_R	0.530	0.33
34_A	37_P	0.527	0.33
7_G	83_F	0.523	0.32
15_I	92_L	0.512	0.31
24_L	40_V	0.512	0.31
56_L	69_L	0.508	0.31
54_Y	62_T	0.508	0.31
29_P	32_Y	0.508	0.31
6_I	88_Y	0.506	0.31
62_T	65_V	0.506	0.31
6_I	65_V	0.506	0.31
19_S	51_F	0.500	0.30

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2xgrA	1	0.0417	3.1	0.942	Contact Map
2qtsA	4	0.3333	2.6	0.945	Contact Map
4w9uA	4	0.3854	1.8	0.949	Contact Map
3sf6A	4	0.3854	1.8	0.949	Contact Map
3ii9A	4	0.3854	1.7	0.95	Contact Map
4hzuS	1	0.9688	1.4	0.952	Contact Map
4tkrA	2	0.9688	1.4	0.952	Contact Map
4m8dA	4	0.5104	1.3	0.953	Contact Map
3b8cA	1	1	1.2	0.954	Contact Map
3a68A	7	0.3021	1.2	0.954	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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